6o7e - Revision history

OCA at 09:23, 20 March 2024

2024-03-20T09:23:08Z

← Older revision		Revision as of 09:23, 20 March 2024
Line 3:		Line 3:
	<SX load='6o7e' size='340' side='right' viewer='molstar' caption='[[6o7e]], [[Resolution\|resolution]] 3.20Å' scene=''>		<SX load='6o7e' size='340' side='right' viewer='molstar' caption='[[6o7e]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6o7e]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Theon Theon~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6O7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[6o7e]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_onnurineus Thermococcus onnurineus] and [https://en.wikipedia.org/wiki/Thermococcus_onnurineus_NA1 Thermococcus onnurineus NA1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6O7E FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>~~, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.2Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~UNK~~:~~UNKNOWN~~'>~~UNK~~</scene><~~/td~~></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></~~td><td class="sblockDat"~~>TON_0893 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0894 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0895 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0896 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0897 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON])</td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6o7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7e OCA], [https://pdbe.org/6o7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6o7e RCSB], [https://www.ebi.ac.uk/pdbsum/6o7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7e ProSAT]</span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6o7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7e OCA], [~~http~~://pdbe.org/6o7e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6o7e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6o7e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7e ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~		== Function ==
	== ~~Publication Abstract from PubMed~~ ==		[https://www.uniprot.org/uniprot/CAS10_THEON CAS10_THEON] CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). The type III-A Csm effector complex binds crRNA and acts as a crRNA-guided RNase, DNase and cyclic oligoadenylate synthase; binding of target RNA cognate to the crRNA is required for all activities.[UniProtKB:A0A0A7HFE1] A single-strand deoxyribonuclease (ssDNase) which digests linear and circular ssDNA; has 5'-3' and 3'-5' exonuclease activity as well as a less efficient endonuclease activity. Has a minimal size requirement; 100 nucleotide ssDNA (nt) is more efficiently digested than 50 or 25 nt ssDNA, while 14 nt ssDNA is not cleaved at all. It has no activity on dsDNA or ssRNA.<ref>PMID:25773141</ref> ssDNase activity is stimulated in the ternary Csm effector complex; binding of cognate target RNA activates the ssDNase, as the target RNA is degraded ssDNA activity decreases.[UniProtKB:A0A0A7HFE1] When associated with the ternary Csm effector complex (the crRNA, Cas proteins and a cognate target ssRNA) synthesizes cyclic oligoadenylates (cOA) from ATP. cOAs are second messengers that stimulate the ssRNase activity of Csm6, inducing an antiviral state important for defense against invading nucleic acids.[UniProtKB:A0A0A7HFE1]
	Target RNA binding to crRNA-bound type III-A CRISPR-Cas multi-subunit Csm surveillance complexes activates cyclic-oligoadenylate (cAn) formation from ATP subunits positioned within the composite pair of Palm domain pockets of the Csm1 subunit. ~~The generated cAn second messenger in turn targets the CARF domain of trans-acting RNase Csm6, triggering its HEPN domain-based RNase activity~~. ~~We have undertaken cryo-EM studies on multi-subunit Thermococcus onnurineus Csm effector ternary complexes, as well as X-ray studies on Csm1-Csm4 cassette, both bound to substrate~~ (~~AMPPNP~~)~~, intermediates~~ (~~pppAn)~~, and ~~products (cAn~~), to ~~decipher mechanistic aspects of cAn formation~~ and ~~release~~. ~~A network of intermolecular hydrogen bond alignments accounts for the observed adenosine specificity, with ligand positioning dictating formation of linear pppAn intermediates~~ and ~~subsequent cAn formation by cyclization. We combine our structural results with published functional studies to highlight mechanistic insights~~ into ~~the role of the Csm effector complex in mediating the cAn signaling pathway~~.

	~~Second Messenger cA4 Formation within the Composite Csm1 Palm Pocket of Type~~ III-A ~~CRISPR-Cas~~ Csm ~~Complex~~ and ~~Its Release Path.~~,~~Jia N, Jones R, Sukenick G, Patel DJ Mol Cell. 2019 Jun 28~~. ~~pii~~: ~~S1097~~-~~2765~~(19)~~30446~~-0. ~~doi:~~, 10.~~1016/j.molcel.2019.06.013~~. ~~PMID:31326272~~<ref>PMID:~~31326272~~</ref>

	~~From MEDLINE®/PubMed&reg~~;, ~~a database of~~ the U.S. ~~National Library~~ of ~~Medicine~~.~~<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 6o7e" style="background-color~~:~~#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 15:
	</SX>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Theon~~]]		[[Category: Thermococcus onnurineus]]
	[[Category: ~~Jia, N~~]]		[[Category: Thermococcus onnurineus NA1]]
	[[Category: ~~Patel, D J~~]]		[[Category: Jia N]]
	[[Category: ~~Cryo-em structure]]~~		[[Category: Patel DJ]]
	~~[[Category: Csm-crrna-target rna ternary complex in complex with amppnp]]~~
	~~[[Category: Immune system]]~~
	~~[[Category: Immune system-rna complex]]~~
	~~[[Category: Type iii crispr-cas systerm~~]]

OCA at 03:46, 11 April 2020

2020-04-11T03:46:08Z

← Older revision		Revision as of 03:46, 11 April 2020
Line 3:		Line 3:
	<SX load='6o7e' size='340' side='right' viewer='molstar' caption='[[6o7e]], [[Resolution\|resolution]] 3.20Å' scene=''>		<SX load='6o7e' size='340' side='right' viewer='molstar' caption='[[6o7e]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6o7e]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Theon Theon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7E OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6O7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[6o7e]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Theon Theon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7E OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6O7E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TON_0893 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0894 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0895 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0896 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0897 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TON_0893 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0894 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0895 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0896 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0897 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6o7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7e OCA], [http://pdbe.org/6o7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o7e RCSB], [http://www.ebi.ac.uk/pdbsum/6o7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7e ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6o7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7e OCA], [http://pdbe.org/6o7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o7e RCSB], [http://www.ebi.ac.uk/pdbsum/6o7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7e ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:01, 6 March 2020

2020-03-06T23:01:09Z

← Older revision		Revision as of 23:01, 6 March 2020
Line 1:		Line 1:

	==Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with AMPPNP in type III-A CRISPR-Cas system==		==Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with AMPPNP in type III-A CRISPR-Cas system==
	<~~StructureSection~~ load='6o7e' size='340' side='right'caption='[[6o7e]], [[Resolution\|resolution]] 3.20Å' scene=''>		<SX load='6o7e' size='340' side='right' viewer='molstar' caption='[[6o7e]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6o7e]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O7E FirstGlance]. <br>		<table><tr><td colspan='2'>[[6o7e]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Theon Theon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O7E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O7E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TON_0893 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0894 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0895 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0896 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON]), TON_0897 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=523850 THEON])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6o7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7e OCA], [http://pdbe.org/6o7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o7e RCSB], [http://www.ebi.ac.uk/pdbsum/6o7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7e ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6o7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o7e OCA], [http://pdbe.org/6o7e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o7e RCSB], [http://www.ebi.ac.uk/pdbsum/6o7e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o7e ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	<references/>		<references/>
	__TOC__		__TOC__
	</~~StructureSection~~>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
			[[Category: Theon]]
	[[Category: Jia, N]]		[[Category: Jia, N]]
	[[Category: Patel, D J]]		[[Category: Patel, D J]]

OCA at 06:25, 31 July 2019

2019-07-31T06:25:32Z

@@ Line 1: / Line 1: @@
-The entry 6o7e is ON HOLD  until Paper Publication
+==Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with AMPPNP in type III-A CRISPR-Cas system==
-Authors:
+Second Messenger cA4 Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path.,Jia N, Jones R, Sukenick G, Patel DJ Mol Cell. 2019 Jun 28. pii: S1097-2765(19)30446-0. doi:, 10.1016/j.molcel.2019.06.013. PMID:31326272<ref>PMID:31326272</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>

OCA at 07:03, 1 May 2019

2019-05-01T07:03:37Z

← Older revision		Revision as of 07:03, 1 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6o7e is ON HOLD		The entry 6o7e is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6o7e" [edit=sysop:move=sysop]

2019-03-13T10:19:21Z

Protected "6o7e" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:19, 13 March 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6o7e is ON HOLD Authors: Description: Category: Unreleased Structures

2019-03-13T10:19:19Z

New page: '''Unreleased structure''' The entry 6o7e is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6o7e is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]